removeAnnoationData {IsoformSwitchAnalyzeR} | R Documentation

## Removes data not needed after switch identification.

### Description

This function can removes the biological sequence and/or the replicate quantification data from a switchAnalyzeRlist which will significantly reduce the size of the object. This is intended to be used after identification of consequnces of isoform switches (via `analyzeSwitchConsequences`) have been done as then these data are not longer needed. It is highly recomended to save a version of the switchAnalyzeRlist with all the annotation before removeing it - typically done with `base::saveRDS` or `base::save`.

### Usage

    removeAnnoationData(
        switchAnalyzeRlist,
        removeBioSeq = TRUE,
        removeQuantData = TRUE
    )

### Arguments

`switchAnalyzeRlist` | A `switchAnalyzeRlist` object where `analyzeSwitchConsequences()` have been run to identify consequences of isoform switches
`removeBioSeq` | A logical indicating whether to remove biological sequences (nucloetide and amino acid sequences) from the switchAnalyzeRlist. Default is TRUE.
`removeQuantData` | A logic indicating whether to remove replicate quantification data (counts, abundances and isoform fractions) from the switchAnalyzeRlist. Default is TRUE.

### Value

This function returns a data.frame where the first column is the gene id followed by the gene expression in all samples.

### Author(s)

Kristoffer Vitting-Seerup

### References

Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Mol. Cancer Res. (2017).

### Examples

    ### Please note
    # 1) The way of importing files in the following example with
    #       "system.file('pathToFile', package="IsoformSwitchAnalyzeR") is
    #       specialiced to access the sample data in the IsoformSwitchAnalyzeR package
    #       and not somhting you need to do - just supply the string e.g.
    #       "/myAnnotation/isoformsQuantified.gtf" to the functions
    # 2) importRdata directly supports import of a GTF file - just supply the
    #       path (e.g. "/myAnnotation/isoformsQuantified.gtf") to the isoformExonAnnoation argument

    ### Import quantifications
    salmonQuant <- importIsoformExpression(system.file("extdata/", package="IsoformSwitchAnalyzeR"))

    ### Make design matrix
    myDesign <- data.frame(
        sampleID = colnames(salmonQuant$abundance)[-1],
        condition = gsub('_.*', '', colnames(salmonQuant$abundance)[-1])
    )

    ### Create switchAnalyzeRlist
    aSwitchList <- importRdata(
        isoformCountMatrix   = salmonQuant$counts,
        isoformRepExpression = salmonQuant$abundance,
        designMatrix         = myDesign,
        isoformExonAnnoation = system.file("extdata/example.gtf.gz", package="IsoformSwitchAnalyzeR")
    )
    names(aSwitchList)

    ### Remove annotation data
    aSwitchList <- removeAnnoationData(aSwitchList)
    names(aSwitchList)

[Package IsoformSwitchAnalyzeR version 1.4.0 Index]